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42 #include "gromacs/commandline/pargs.h"
43 #include "gromacs/gmxana/gmx_ana.h"
44 #include "gromacs/gmxana/sfactor.h"
45 #include "gromacs/utility/arraysize.h"
46 #include "gromacs/utility/pleasecite.h"
47 #include "gromacs/utility/smalloc.h"
49 int gmx_saxs(int argc, char* argv[])
51 const char* desc[] = { "[THISMODULE] calculates SAXS structure factors for given index",
52 "groups based on Cromer's method.",
53 "Both topology and trajectory files are required." };
55 static real start_q = 0.0, end_q = 60.0, energy = 12.0;
56 static int ngroups = 1;
59 { "-ng", FALSE, etINT, { &ngroups }, "Number of groups to compute SAXS" },
60 { "-startq", FALSE, etREAL, { &start_q }, "Starting q (1/nm) " },
61 { "-endq", FALSE, etREAL, { &end_q }, "Ending q (1/nm)" },
62 { "-energy", FALSE, etREAL, { &energy }, "Energy of the incoming X-ray (keV) " }
65 const char * fnTPS, *fnTRX, *fnNDX, *fnDAT = nullptr;
66 gmx_output_env_t* oenv;
69 { efTRX, "-f", nullptr, ffREAD }, { efTPS, nullptr, nullptr, ffREAD },
70 { efNDX, nullptr, nullptr, ffOPTRD }, { efDAT, "-d", "sfactor", ffOPTRD },
71 { efXVG, "-sq", "sq", ffWRITE },
73 #define NFILE asize(fnm)
74 if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm, NPA, pa, asize(desc), desc, 0,
80 fnTPS = ftp2fn(efTPS, NFILE, fnm);
81 fnTRX = ftp2fn(efTRX, NFILE, fnm);
82 fnDAT = ftp2fn(efDAT, NFILE, fnm);
83 fnNDX = ftp2fn_null(efNDX, NFILE, fnm);
85 do_scattering_intensity(fnTPS, fnNDX, opt2fn("-sq", NFILE, fnm), fnTRX, fnDAT, start_q, end_q,
86 energy, ngroups, oenv);
88 please_cite(stdout, "Cromer1968a");